Align Indolepyruvate oxidoreductase subunit IorA; IOR; Indolepyruvate ferredoxin oxidoreductase subunit alpha; EC 1.2.7.8 (characterized)
to candidate 207421 DVU1951 indolepyruvate ferredoxin oxidoreductase, alpha subunit, putative
Query= SwissProt::P80910 (618 letters) >MicrobesOnline__882:207421 Length = 616 Score = 476 bits (1224), Expect = e-138 Identities = 270/605 (44%), Positives = 365/605 (60%), Gaps = 20/605 (3%) Query: 12 GDRLFLLGNEAAVRAAIESGVGVASTYPGTPSSEIGNVLSKIAKRAGIYFEFSINEKVAL 71 G+R LLGNEA VR A+E+G+ V + YPGTPSSE+ + +I E+S+NEKVAL Sbjct: 11 GERHLLLGNEAIVRGALEAGINVVTCYPGTPSSEVPDTFRRIGGDGRYRLEYSVNEKVAL 70 Query: 72 EVAAAAAASGVRSFTFMKHVGLNVASDSFMSVAYTGVRAGMVVLSADDPSMFSSQNEQDN 131 EV A AA +G + MKHVG+NVA+D +++ YTG+ G+V+LSADDP SSQNEQDN Sbjct: 71 EVGAGAALAGALTLVTMKHVGVNVAADPLLTMTYTGLPGGLVLLSADDPGCHSSQNEQDN 130 Query: 132 RHYARLAWVPLLEPSNPQEILEYMNHAFELSEEYRIPVLLRTTTRVSHMRGVVEAGERRA 191 R YAR A +P EP+ QE + A LS E + PVLLRTTTRV+H+RG V G Sbjct: 131 RTYARFAGMPCFEPATAQEAKDMAREALLLSRETQQPVLLRTTTRVNHLRGGVTYGALPE 190 Query: 192 EPVKGFFRKNPEQFVPVPATARVMRRELVEKMKKLKRVADTSELNRVLNEDSESDLGIIA 251 F +NP +FVPVPA AR + + ++ +A S N V E +G+IA Sbjct: 191 PAAVVPFERNPRRFVPVPAVARARHFAQADVLGRVAELASASPWNTV---HGEGRIGVIA 247 Query: 252 SGGAFNYVYDALQTLGLD--VPVLKLGFTYPFPAGLVAEFLSGLEGVLVVEEVDSVMEKE 309 SG + Y+ DAL GL+ V VL+LGFT+P P L+ +FLSG + VLV+EE++ ++E++ Sbjct: 248 SGISRAYLADALHERGLEGRVKVLELGFTWPLPERLLVDFLSGCDKVLVLEELEPLLERD 307 Query: 310 VLAVATSEGLDVGVHGKLDGTLPEIYEYSEDIVRRAISGLTGIKSHEKGIEAP-----EL 364 V A+ GL V V GK G L EYS IV A+S G +P EL Sbjct: 308 VRALVQRLGLGVDVTGK-GGVLTVFGEYSTTIVGDALSAFLGETPAAPVQCSPDAASMEL 366 Query: 365 PERPPALCPGCPHRAMYYSVRRAASELGIEGEDLIFPTDIGCYTLGIEPPYSAADYLLSM 424 P RPP LC GC HRA+YY+VR+ + G+D + +DIGCYTLG+ PP S AD+L M Sbjct: 367 PMRPPNLCAGCSHRAVYYAVRK------VFGDDAYYSSDIGCYTLGLLPPLSMADFLFCM 420 Query: 425 GSSVGTACGFSAATSQRIVSFIGDSTFFHAGIPPLINAVHNRQRFVLVILDNRTTAMTGG 484 GSS+ + GF+AA+ + +V++IGDSTFFH+GI L NA+ N+ ++VILDN TTAMTG Sbjct: 421 GSSISSGSGFAAASGRPVVAYIGDSTFFHSGITGLANALFNKHDVLVVILDNGTTAMTGH 480 Query: 485 QPHPGLPVDGMGEEAPAISIEDITRACGVEFVETVNPMNIRRSSETIRRALQHESVAVVI 544 QP+PG+ +G+ + IE I R CGVE V TV+P N++ + + Q V V+I Sbjct: 481 QPNPGVDAAVLGDACLHLDIEAIVRGCGVEQVATVHPYNLKATMAALEDMKQRTGVRVII 540 Query: 545 SRYPCMLSEGAVRGRPVRVDEEKCDLCLE---CLNELACPAIVEEDGRVFIDPLYCRGCT 601 ++ PC+L + R + E CL ELACPA + + ID C GC Sbjct: 541 AQEPCVLYARRTLKKAARQTAYVAEQGPEVEACLAELACPAFRRDGQDIAIDSEQCSGCM 600 Query: 602 ICLQI 606 +CLQ+ Sbjct: 601 VCLQV 605 Lambda K H 0.319 0.137 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 902 Number of extensions: 36 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 618 Length of database: 616 Length adjustment: 37 Effective length of query: 581 Effective length of database: 579 Effective search space: 336399 Effective search space used: 336399 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory